doc: describe heuristic

modules/conop/doc/connectivity.rst

@@ -40,14 +40,19 @@ Processors
 The exact behaviour for a processor is implementation-specific. So far, two
 classes implement the processor interface: A heuristic and a rule-based
 processor. The processors mainly differ in the source of their connectivity
-information. The `HeuristicProcessor` uses a hard-coded heuristic connectivity
+information. 
+
+The `HeuristicProcessor` uses a hard-coded heuristic connectivity
 table for the 20  standard amino acids as well as nucleotides. For other
 compounds such as ligands the `HeuristicProcessor` runs a distance-based
-connectivity algorithm that connects two atoms if they are closer than a certain
-threshold. The `RuleBasedProcessor` uses the
-:doc:`compound library <compoundlib>`, a connectivity library containing all
-molecular components present in the PDB files on PDB.org. The library can easily
-be extended with custom  connectivity information, if required.
+connectivity algorithm that connects two atoms if they belong to the same or
+two consecutive residues, and are within a 
+:func:`reasonable distance <ost.conop.IsBondFeasible>` of each other.
+
+The `RuleBasedProcessor` uses the :doc:`compound library <compoundlib>`,
+a connectivity library containing all molecular components present in the
+PDB files on PDB.org. The library can easily be extended with custom
+connectivity information, if required.
 
 
 .. class:: Processor

modules/conop/doc/functions.rst

@@ -33,9 +33,12 @@ Conop Functions
 
 .. function:: IsBondFeasible(atom_a, atom_b)
 
-  :return: True, if *atom_a* and *atom_b* are within a reasonable distance for a
-           bond to be present. Depends on :attr:`~ost.mol.AtomHandle.radius` of
-           atoms and heuristic formulas.
+  :return: True, if *atom_a* and *atom_b* are within a reasonable distance for
+           a bond to be present, namely if the distance between the two atoms
+           is between 0.0625 and 0.375 times the square of the sum of the 
+           :attr:`van der Waals radii <ost.mol.AtomHandle.radius>` of the two
+           atom.
+
   :rtype:  :class:`bool`
   :param atom_a: Atom to be checked.
   :type atom_a:  :class:`~ost.mol.AtomHandle`